Construct Non-Hierarchical P/NBD Model for Online Retail Transaction Data

In this workbook we construct our first hierarchical P/NBD models on the synthetic data with the longer timeframe.

1 Load and Construct Datasets

We start by modelling the P/NBD model using our synthetic datasets before we try to model real-life data.

1.1 Load Online Retail Data

We now want to load the online retail transaction data.

Code

customer_cohortdata_tbl <- read_rds("data/onlineretail_cohort_tbl.rds")
customer_cohortdata_tbl |> glimpse()

Rows: 5,852
Columns: 5
$ customer_id     <chr> "12346", "12347", "12348", "12349", "12350", "12351", …
$ cohort_qtr      <chr> "2010 Q1", "2010 Q4", "2010 Q3", "2010 Q2", "2011 Q1",…
$ cohort_ym       <chr> "2010 03", "2010 10", "2010 09", "2010 04", "2011 02",…
$ first_tnx_date  <date> 2010-03-02, 2010-10-31, 2010-09-27, 2010-04-29, 2011-…
$ total_tnx_count <int> 3, 8, 5, 3, 1, 1, 9, 2, 1, 2, 6, 2, 5, 10, 6, 4, 10, 2…

Code

customer_transactions_tbl <- read_rds("data/onlineretail_transactions_tbl.rds")
customer_transactions_tbl |> glimpse()

Rows: 36,658
Columns: 4
$ tnx_timestamp <dttm> 2009-12-01 07:45:00, 2009-12-01 07:45:59, 2009-12-01 09…
$ customer_id   <fct> 13085, 13085, 13078, 15362, 18102, 12682, 18087, 18087, …
$ invoice_id    <chr> "489434", "489435", "489436", "489437", "489438", "48943…
$ tnx_amount    <dbl> 505.30, 145.80, 630.33, 310.75, 2286.24, 372.30, 50.40, …

Code

customer_subset_id <- read_rds("data/onlineretail_customer_subset_ids.rds")
customer_subset_id |> glimpse()

 Factor w/ 5852 levels "13085","13078",..: 2 3 8 10 14 16 17 21 27 30 ...

1.2 Load Derived Data

Code

customer_summarystats_tbl <- read_rds("data/onlineretail_customer_summarystats_tbl.rds")

obs_fitdata_tbl   <- read_rds("data/onlineretail_obs_fitdata_tbl.rds")
obs_validdata_tbl <- read_rds("data/onlineretail_obs_validdata_tbl.rds")

customer_fit_stats_tbl <- obs_fitdata_tbl |>
  rename(x = tnx_count)

1.3 Load Subset Data

We also want to construct our data subsets for the purposes of speeding up our valuations.

Code

customer_fit_subset_tbl <- obs_fitdata_tbl |>
  filter(customer_id %in% customer_subset_id)

customer_fit_subset_tbl |> glimpse()

Rows: 1,000
Columns: 6
$ customer_id    <fct> 13078, 15362, 14110, 13758, 17592, 13767, 17238, 17700,…
$ first_tnx_date <dttm> 2009-12-01 09:05:59, 2009-12-01 09:08:00, 2009-12-01 0…
$ last_tnx_date  <dttm> 2010-11-30 13:17:59, 2010-09-17 10:36:59, 2010-09-30 1…
$ tnx_count      <dbl> 30, 1, 20, 6, 0, 35, 14, 9, 4, 9, 78, 2, 17, 5, 22, 2, …
$ t_x            <dbl> 52.02500, 41.43740, 43.32966, 51.72589, 0.00000, 52.034…
$ T_cal          <dbl> 52.08869, 52.08849, 52.08433, 52.08274, 52.07847, 52.07…

Code

customer_valid_subset_tbl <- obs_validdata_tbl |>
  filter(customer_id %in% customer_subset_id)

customer_valid_subset_tbl |> glimpse()

Rows: 1,000
Columns: 3
$ customer_id       <fct> 13078, 15362, 14110, 13758, 17592, 13767, 17238, 177…
$ tnx_count         <dbl> 26, 0, 12, 7, 0, 37, 17, 4, 4, 13, 48, 0, 13, 3, 16,…
$ tnx_last_interval <dbl> 52.950000, NA, 52.931151, 51.780853, NA, 53.089286, …

We now use these datasets to set the start and end dates for our various validation methods.

Code

dates_lst <- read_rds("data/onlineretail_simulation_dates.rds")

use_fit_start_date <- dates_lst$use_fit_start_date
use_fit_end_date   <- dates_lst$use_fit_end_date

use_valid_start_date <- dates_lst$use_valid_start_date
use_valid_end_date   <- dates_lst$use_valid_end_date

We now split out the transaction data into fit and validation datasets.

Code

customer_fit_transactions_tbl <- customer_transactions_tbl |>
  filter(
    customer_id %in% customer_subset_id,
    tnx_timestamp >= use_fit_start_date,
    tnx_timestamp <= use_fit_end_date
    )
  
customer_fit_transactions_tbl |> glimpse()

Rows: 4,164
Columns: 4
$ tnx_timestamp <dttm> 2009-12-01 09:05:59, 2009-12-01 09:08:00, 2009-12-01 09…
$ customer_id   <fct> 13078, 15362, 14110, 13758, 17592, 13767, 17238, 17700, …
$ invoice_id    <chr> "489436", "489437", "489443", "489446", "489462", "48946…
$ tnx_amount    <dbl> 630.33, 310.75, 285.06, 996.10, 148.30, 1197.80, 251.10,…

Code

customer_valid_transactions_tbl <- customer_transactions_tbl |>
  filter(
    customer_id %in% customer_subset_id,
    tnx_timestamp >= use_valid_start_date,
    tnx_timestamp <= use_valid_end_date
    )
  
customer_valid_transactions_tbl |> glimpse()

Rows: 3,422
Columns: 4
$ tnx_timestamp <dttm> 2010-12-01 09:32:00, 2010-12-01 09:59:00, 2010-12-01 10…
$ customer_id   <fct> 15291, 16250, 12431, 13408, 13767, 12791, 17908, 16583, …
$ invoice_id    <chr> "536376", "536388", "536389", "536394", "536395", "53640…
$ tnx_amount    <dbl> 657.60, 452.28, 716.50, 2049.36, 1015.76, 355.20, 486.56…

Finally, we want to extract the first transaction for each customer, so we can add this data to assess our models.

Code

customer_initial_tnx_tbl <- customer_fit_transactions_tbl |>
  slice_min(n = 1, order_by = tnx_timestamp, by = customer_id)

customer_initial_tnx_tbl |> glimpse()

Rows: 1,002
Columns: 4
$ tnx_timestamp <dttm> 2009-12-01 09:05:59, 2009-12-01 09:08:00, 2009-12-01 09…
$ customer_id   <fct> 13078, 15362, 14110, 13758, 17592, 13767, 17238, 17700, …
$ invoice_id    <chr> "489436", "489437", "489443", "489446", "489462", "48946…
$ tnx_amount    <dbl> 630.33, 310.75, 285.06, 996.10, 148.30, 1197.80, 251.10,…

We now expand out these initial transactions so that we can append them to our simulations.

Code

sim_init_tbl <- customer_initial_tnx_tbl |>
  transmute(
    customer_id,
    draw_id       = list(1:n_sim),
    tnx_timestamp,
    tnx_amount
    ) |>
  unnest(draw_id)

sim_init_tbl |> glimpse()

Rows: 2,004,000
Columns: 4
$ customer_id   <fct> 13078, 13078, 13078, 13078, 13078, 13078, 13078, 13078, …
$ draw_id       <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1…
$ tnx_timestamp <dttm> 2009-12-01 09:05:59, 2009-12-01 09:05:59, 2009-12-01 09…
$ tnx_amount    <dbl> 630.33, 630.33, 630.33, 630.33, 630.33, 630.33, 630.33, …

Before we start on that, we set a few parameters for the workbook to organise our Stan code.

Code

stan_modeldir <- "stan_models"
stan_codedir  <-   "stan_code"

2 Fit First P/NBD Model

We now construct our Stan model and prepare to fit it with our synthetic dataset.

We also want to set a number of overall parameters for this workbook

To start the fit data, we want to use the 1,000 customers. We also need to calculate the summary statistics for the validation period.

2.1 Compile and Fit Stan Model

We now compile this model using CmdStanR.

Code

pnbd_fixed_stanmodel <- cmdstan_model(
  "stan_code/pnbd_fixed.stan",
  include_paths =   stan_codedir,
  pedantic      =           TRUE,
  dir           =  stan_modeldir
  )

We then use this compiled model with our data to produce a fit of the data.

Code

stan_modelname <- "pnbd_onlineretail_fixed1"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")

stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 1.00,
    
    mu_mn     = 0.10,
    mu_cv     = 1.00,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_onlineretail_fixed1_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )
  
  pnbd_onlineretail_fixed1_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_onlineretail_fixed1_stanfit <- read_rds(stanfit_object_file)
}

pnbd_onlineretail_fixed1_stanfit$print()

  variable      mean    median    sd   mad        q5       q95 rhat ess_bulk
 lp__      -68219.16 -68217.50 69.77 71.09 -68336.81 -68107.27 1.00      696
 lambda[1]      0.41      0.39  0.18  0.17      0.16      0.76 1.00     1439
 lambda[2]      0.56      0.55  0.10  0.10      0.41      0.73 1.00     2156
 lambda[3]      0.04      0.03  0.03  0.02      0.01      0.09 1.00     1905
 lambda[4]      1.53      1.52  0.17  0.17      1.26      1.83 1.00     1925
 lambda[5]      0.36      0.35  0.08  0.08      0.24      0.50 1.00     2091
 lambda[6]      0.27      0.26  0.07  0.07      0.16      0.39 1.00     2114
 lambda[7]      0.06      0.05  0.03  0.03      0.02      0.12 1.00     2823
 lambda[8]      0.41      0.40  0.09  0.09      0.28      0.56 1.01     2300
 lambda[9]      0.17      0.16  0.06  0.05      0.09      0.27 1.00     2050
 ess_tail
     1198
      981
     1452
     1041
     1501
     1374
     1537
     1146
     1588
     1636

 # showing 10 of 12718 rows (change via 'max_rows' argument or 'cmdstanr_max_rows' option)

We have some basic HMC-based validity statistics we can check.

Code

pnbd_onlineretail_fixed1_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed1-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed1-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed1-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed1-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

2.2 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_onlineretail_fixed1_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We also check \(N_{eff}\) as a quick diagnostic of the fit.

Code

pnbd_onlineretail_fixed1_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

Finally, we want to check out the energy diagnostic, which is often indicative of problems with the posterior mixing.

Code

pnbd_onlineretail_fixed1_stanfit |>
  nuts_params() |>
  mcmc_nuts_energy(binwidth = 50)

2.3 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

Code

pnbd_stanfit <- pnbd_onlineretail_fixed1_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_onlineretail_fixed1_assess_data_lst <- run_model_assessment(
  model_stanfit    = pnbd_stanfit,
  insample_tbl     = customer_fit_subset_tbl,
  fit_label        = "pnbd_onlineretail_fixed1",
  fit_end_dttm     = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm   = use_valid_end_date   |> as.POSIXct(),
  sim_seed         = 1010
  )

pnbd_onlineretail_fixed1_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_onlineretail_fixed1_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_onlineretail_fixed1_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_onlineretail_fixed1_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_onlineretail_fixed1_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_onlineretail_fixed1_assess_valid_simstats_tbl.rds"

2.3.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed1_assess_data_lst |>
  use_series(model_fit_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  bind_rows(sim_init_tbl) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

2.3.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed1_assess_data_lst |>
  use_series(model_valid_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

As for our short time frame data, overall our model is working well.

           used  (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells  3740042 199.8   41183656 2199.5  64349462 3436.7
Vcells 91246295 696.2  270874437 2066.7 258678648 1973.6

3 Fit Alternate Prior Model.

We want to try an alternate prior model with a smaller co-efficient of variation to see what impact it has on our procedures.

Code

stan_modelname <- "pnbd_onlineretail_fixed2"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")

stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 0.50,
    
    mu_mn     = 0.10,
    mu_cv     = 0.50,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_onlineretail_fixed2_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )
  
  pnbd_onlineretail_fixed2_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_onlineretail_fixed2_stanfit <- read_rds(stanfit_object_file)
}

pnbd_onlineretail_fixed2_stanfit$print()

  variable       mean     median    sd   mad         q5        q95 rhat
 lp__      -144230.90 -144230.00 69.17 68.20 -144348.00 -144118.00 1.01
 lambda[1]       0.34       0.33  0.12  0.11       0.17       0.55 1.01
 lambda[2]       0.50       0.49  0.09  0.09       0.36       0.65 1.00
 lambda[3]       0.08       0.07  0.04  0.03       0.03       0.14 1.00
 lambda[4]       1.30       1.30  0.14  0.14       1.07       1.54 1.00
 lambda[5]       0.34       0.33  0.07  0.07       0.23       0.46 1.00
 lambda[6]       0.26       0.26  0.06  0.06       0.17       0.37 1.00
 lambda[7]       0.09       0.09  0.04  0.04       0.04       0.17 1.00
 lambda[8]       0.38       0.38  0.08  0.07       0.27       0.52 1.01
 lambda[9]       0.19       0.18  0.06  0.06       0.11       0.29 1.00
 ess_bulk ess_tail
      613     1051
     3911     1343
     5498     1341
     4314     1519
     5548     1348
     5048     1376
     3364     1070
     4360      935
     4123     1418
     4274     1328

 # showing 10 of 12718 rows (change via 'max_rows' argument or 'cmdstanr_max_rows' option)

We have some basic HMC-based validity statistics we can check.

Code

pnbd_onlineretail_fixed2_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed2-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed2-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed2-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed2-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

3.1 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_onlineretail_fixed2_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We want to check the \(N_{eff}\) statistics also.

Code

pnbd_onlineretail_fixed2_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

Finally, we want to check out the energy diagnostic, which is often indicative of problems with the posterior mixing.

Code

pnbd_onlineretail_fixed2_stanfit |>
  nuts_params() |>
  mcmc_nuts_energy(binwidth = 50)

3.2 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

Code

pnbd_stanfit <- pnbd_onlineretail_fixed2_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_onlineretail_fixed2_assess_data_lst <- run_model_assessment(
  model_stanfit    = pnbd_stanfit,
  insample_tbl     = customer_fit_subset_tbl,
  fit_label        = "pnbd_onlineretail_fixed2",
  fit_end_dttm     = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm   = use_valid_end_date   |> as.POSIXct(),
  sim_seed         = 1020
  )

pnbd_onlineretail_fixed2_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_onlineretail_fixed2_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_onlineretail_fixed2_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_onlineretail_fixed2_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_onlineretail_fixed2_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_onlineretail_fixed2_assess_valid_simstats_tbl.rds"

3.2.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed2_assess_data_lst |>
  use_series(model_fit_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  bind_rows(sim_init_tbl) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

3.2.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed2_assess_data_lst |>
  use_series(model_valid_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

            used  (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells   3774548 201.6   30357408 1621.3  64349462 3436.7
Vcells 126822914 967.6  325129324 2480.6 312087871 2381.1

4 Fit Tight-Lifetime Model

We now want to try a model where we use priors with a tighter coefficient of variation for lifetime but keep the CoV for transaction frequency.

Code

stan_modelname <- "pnbd_onlineretail_fixed3"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")


stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 1.00,
    
    mu_mn     = 0.10,
    mu_cv     = 0.50,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_onlineretail_fixed3_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )
  
  pnbd_onlineretail_fixed3_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_onlineretail_fixed3_stanfit <- read_rds(stanfit_object_file)
}

pnbd_onlineretail_fixed3_stanfit$print()

  variable       mean     median    sd   mad         q5        q95 rhat
 lp__      -112036.12 -112037.00 68.86 69.68 -112148.00 -111923.00 1.01
 lambda[1]       0.41       0.39  0.18  0.17       0.17       0.74 1.00
 lambda[2]       0.55       0.55  0.10  0.10       0.40       0.73 1.00
 lambda[3]       0.04       0.03  0.03  0.02       0.01       0.09 1.00
 lambda[4]       1.54       1.53  0.17  0.17       1.28       1.82 1.00
 lambda[5]       0.36       0.35  0.08  0.08       0.24       0.49 1.00
 lambda[6]       0.27       0.26  0.07  0.07       0.17       0.39 1.00
 lambda[7]       0.06       0.05  0.03  0.03       0.02       0.12 1.00
 lambda[8]       0.42       0.41  0.10  0.09       0.27       0.59 1.00
 lambda[9]       0.17       0.17  0.06  0.06       0.09       0.28 1.00
 ess_bulk ess_tail
      605      897
     2596     1124
     2939     1510
     1847      969
     2530     1400
     2397     1466
     2663     1517
     1925      855
     2484     1288
     3076     1419

 # showing 10 of 12718 rows (change via 'max_rows' argument or 'cmdstanr_max_rows' option)

We have some basic HMC-based validity statistics we can check.

Code

pnbd_onlineretail_fixed3_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed3-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed3-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed3-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed3-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

4.1 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_onlineretail_fixed3_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We want to check the \(N_{eff}\) statistics also.

Code

pnbd_onlineretail_fixed3_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

Finally, we want to check out the energy diagnostic, which is often indicative of problems with the posterior mixing.

Code

pnbd_onlineretail_fixed3_stanfit |>
  nuts_params() |>
  mcmc_nuts_energy(binwidth = 50)

4.2 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

Code

pnbd_stanfit <- pnbd_onlineretail_fixed3_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_onlineretail_fixed3_assess_data_lst <- run_model_assessment(
  model_stanfit    = pnbd_stanfit,
  insample_tbl     = customer_fit_subset_tbl,
  fit_label        = "pnbd_onlineretail_fixed3",
  fit_end_dttm     = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm   = use_valid_end_date   |> as.POSIXct(),
  sim_seed         = 1030
  )

pnbd_onlineretail_fixed3_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_onlineretail_fixed3_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_onlineretail_fixed3_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_onlineretail_fixed3_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_onlineretail_fixed3_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_onlineretail_fixed3_assess_valid_simstats_tbl.rds"

4.2.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed3_assess_data_lst |>
  use_series(model_fit_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  bind_rows(sim_init_tbl) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

4.2.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed3_assess_data_lst |>
  use_series(model_valid_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

            used   (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells   3810473  203.6   28043578 1497.7  64349462 3436.7
Vcells 176755948 1348.6  325129324 2480.6 325129322 2480.6

5 Fit Narrow-Short-Lifetime Model

We now want to try a model where we use priors with a tighter coefficient of variation for lifetime but keep the CoV for transaction frequency.

Code

stan_modelname <- "pnbd_onlineretail_fixed4"
stanfit_seed   <- stanfit_seed + 1
stanfit_prefix <- str_c("fit_", stan_modelname) 

stanfit_object_file <- glue("data/{stanfit_prefix}_stanfit.rds")


stan_data_lst <- customer_fit_stats_tbl |>
  select(customer_id, x, t_x, T_cal) |>
  compose_data(
    lambda_mn = 0.25,
    lambda_cv = 1.00,
    
    mu_mn     = 0.20,
    mu_cv     = 0.30,
    )

if(!file_exists(stanfit_object_file)) {
  pnbd_onlineretail_fixed4_stanfit <- pnbd_fixed_stanmodel$sample(
    data            =                stan_data_lst,
    chains          =                            4,
    iter_warmup     =                          500,
    iter_sampling   =                          500,
    seed            =                 stanfit_seed,
    save_warmup     =                         TRUE,
    output_dir      =                stan_modeldir,
    output_basename =               stanfit_prefix,
    )
  
  pnbd_onlineretail_fixed4_stanfit$save_object(stanfit_object_file, compress = "gzip")

} else {
  pnbd_onlineretail_fixed4_stanfit <- read_rds(stanfit_object_file)
}

pnbd_onlineretail_fixed4_stanfit$print()

  variable       mean     median    sd   mad         q5        q95 rhat
 lp__      -184742.84 -184743.00 72.60 71.16 -184864.00 -184622.00 1.00
 lambda[1]       0.43       0.41  0.18  0.18       0.18       0.77 1.00
 lambda[2]       0.55       0.55  0.10  0.09       0.40       0.73 1.00
 lambda[3]       0.04       0.03  0.03  0.02       0.01       0.09 1.00
 lambda[4]       1.55       1.54  0.17  0.17       1.29       1.84 1.01
 lambda[5]       0.36       0.35  0.08  0.07       0.24       0.49 1.00
 lambda[6]       0.27       0.26  0.07  0.07       0.17       0.39 1.00
 lambda[7]       0.06       0.05  0.03  0.03       0.02       0.12 1.00
 lambda[8]       0.42       0.42  0.10  0.09       0.28       0.59 1.00
 lambda[9]       0.18       0.17  0.06  0.05       0.10       0.29 1.00
 ess_bulk ess_tail
      613      989
     4445     1065
     3054     1464
     3003     1042
     3459     1511
     3450     1363
     2932     1278
     2269     1175
     4148     1360
     3464     1572

 # showing 10 of 12718 rows (change via 'max_rows' argument or 'cmdstanr_max_rows' option)

We have some basic HMC-based validity statistics we can check.

Code

pnbd_onlineretail_fixed4_stanfit$cmdstan_diagnose()

Processing csv files: /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed4-1.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed4-2.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed4-3.csvWarning: non-fatal error reading adaptation data
, /home/rstudio/btydwork/stan_models/fit_pnbd_onlineretail_fixed4-4.csvWarning: non-fatal error reading adaptation data


Checking sampler transitions treedepth.
Treedepth satisfactory for all transitions.

Checking sampler transitions for divergences.
No divergent transitions found.

Checking E-BFMI - sampler transitions HMC potential energy.
E-BFMI satisfactory.

Effective sample size satisfactory.

Split R-hat values satisfactory all parameters.

Processing complete, no problems detected.

5.1 Visual Diagnostics of the Sample Validity

Now that we have a sample from the posterior distribution we need to create a few different visualisations of the diagnostics.

Code

parameter_subset <- c(
  "lambda[1]", "lambda[2]", "lambda[3]", "lambda[4]",
  "mu[1]",     "mu[2]",     "mu[3]",     "mu[4]"
  )

pnbd_onlineretail_fixed4_stanfit$draws(inc_warmup = FALSE) |>
  mcmc_trace(pars = parameter_subset) +
  expand_limits(y = 0) +
  labs(
    x = "Iteration",
    y = "Value",
    title = "Traceplot of Sample of Lambda and Mu Values"
    ) +
  theme(axis.text.x = element_text(size = 10))

We want to check the \(N_{eff}\) statistics also.

Code

pnbd_onlineretail_fixed4_stanfit |>
  neff_ratio(pars = c("lambda", "mu")) |>
  mcmc_neff() +
    ggtitle("Plot of Parameter Effective Sample Sizes")

Finally, we want to check out the energy diagnostic, which is often indicative of problems with the posterior mixing.

Code

pnbd_onlineretail_fixed4_stanfit |>
  nuts_params() |>
  mcmc_nuts_energy(binwidth = 50)

5.2 Assess the Model

As we intend to run the same logic to assess each of our models, we have combined all this logic into a single function run_model_assessment, to run the simulations and combine the datasets.

Code

pnbd_stanfit <- pnbd_onlineretail_fixed4_stanfit |>
  recover_types(customer_fit_stats_tbl)

pnbd_onlineretail_fixed4_assess_data_lst <- run_model_assessment(
  model_stanfit    = pnbd_stanfit,
  insample_tbl     = customer_fit_subset_tbl,
  fit_label        = "pnbd_onlineretail_fixed4",
  fit_end_dttm     = use_fit_end_date     |> as.POSIXct(),
  valid_start_dttm = use_valid_start_date |> as.POSIXct(),
  valid_end_dttm   = use_valid_end_date   |> as.POSIXct(),
  sim_seed         = 1040
  )

pnbd_onlineretail_fixed4_assess_data_lst |> glimpse()

List of 5
 $ model_fit_index_filepath     : 'glue' chr "data/pnbd_onlineretail_fixed4_assess_fit_index_tbl.rds"
 $ model_valid_index_filepath   : 'glue' chr "data/pnbd_onlineretail_fixed4_assess_valid_index_tbl.rds"
 $ model_simstats_filepath      : 'glue' chr "data/pnbd_onlineretail_fixed4_assess_model_simstats_tbl.rds"
 $ model_fit_simstats_filepath  : 'glue' chr "data/pnbd_onlineretail_fixed4_assess_fit_simstats_tbl.rds"
 $ model_valid_simstats_filepath: 'glue' chr "data/pnbd_onlineretail_fixed4_assess_valid_simstats_tbl.rds"

5.2.1 Check In-Sample Data Validation

We first check the model against the in-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed4_assess_data_lst |>
  use_series(model_fit_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  bind_rows(sim_init_tbl) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_fit_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

This fit looks reasonable and appears to capture most of the aspects of the data used to fit it. Given that this is a synthetic dataset, this is not surprising, but at least we appreciate that our model is valid.

5.2.2 Check Out-of-Sample Data Validation

We now repeat for the out-of-sample data.

Code

simdata_tbl <- pnbd_onlineretail_fixed4_assess_data_lst |>
  use_series(model_valid_index_filepath) |>
  read_rds() |>
  use_series(sim_file) |>
  map_dfr(read_rds) |>
  select(customer_id, draw_id, sim_data) |>
  unnest(sim_data) |>
  arrange(customer_id, draw_id, tnx_timestamp)


assess_plots_lst <- create_model_assessment_plots(
  obsdata_tbl = customer_valid_transactions_tbl,
  simdata_tbl = simdata_tbl
  )

assess_plots_lst |> map(print)

$total_plot

$quant_plot

            used   (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells   3844676  205.4   36927827 1972.2  64349462 3436.7
Vcells 220341178 1681.1  390235188 2977.3 390235188 2977.3

6 Compare Model Outputs

We have looked at each of the models individually, but it is also worth looking at each of the models as a group.

We now want to combine both the fit and valid transaction sets to calculate the summary statistics for both.

Code

obs_summstats_tbl <- list(
    fit   = customer_fit_transactions_tbl,
    valid = customer_valid_transactions_tbl
    ) |>
  bind_rows(.id = "assess_type") |>
  group_by(assess_type) |>
  calculate_transaction_summary_statistics() |>
  pivot_longer(
    cols      = !assess_type,
    names_to  = "label",
    values_to = "obs_value"
    )

obs_summstats_tbl |> glimpse()

Rows: 16
Columns: 3
$ assess_type <chr> "fit", "fit", "fit", "fit", "fit", "fit", "fit", "fit", "v…
$ label       <chr> "p10", "p25", "p50", "p75", "p90", "p99", "total_count", "…
$ obs_value   <dbl> 1.000000, 1.000000, 2.000000, 5.000000, 9.000000, 27.01000…

Code

model_assess_transactions_tbl <- dir_ls("data", regexp = "pnbd_onlineretail_fixed.*_assess_.*index") |>
  enframe(name = NULL, value = "file_path") |>
  mutate(
    model_label = str_replace(file_path, "data/pnbd_onlineretail_(.*?)_assess_.*", "\\1"),
    assess_type = if_else(str_detect(file_path, "_assess_fit_"), "fit", "valid"),
    
    assess_data = map(
      file_path, construct_model_assessment_data,
      
      .progress = "construct_assess_data"
      )
    ) |>
  select(model_label, assess_type, assess_data) |>
  unnest(assess_data)

model_assess_transactions_tbl |> glimpse()

Rows: 34,590,018
Columns: 6
$ model_label   <chr> "fixed1", "fixed1", "fixed1", "fixed1", "fixed1", "fixed…
$ assess_type   <chr> "fit", "fit", "fit", "fit", "fit", "fit", "fit", "fit", …
$ customer_id   <fct> 13078, 13078, 13078, 13078, 13078, 13078, 13078, 13078, …
$ draw_id       <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
$ tnx_timestamp <dttm> 2009-12-12 19:15:15, 2009-12-17 19:57:58, 2010-01-07 00…
$ tnx_amount    <dbl> 181.28, 8.86, 109.95, 50.98, 146.65, 182.68, 67.32, 42.0…

We now want to calculate the transaction statistics on this full dataset, for each separate draw.

Code

model_assess_tbl <- model_assess_transactions_tbl |>
  group_by(model_label, assess_type, draw_id) |>
  calculate_transaction_summary_statistics()

model_assess_tbl |> glimpse()

Rows: 16,000
Columns: 11
$ model_label <chr> "fixed1", "fixed1", "fixed1", "fixed1", "fixed1", "fixed1"…
$ assess_type <chr> "fit", "fit", "fit", "fit", "fit", "fit", "fit", "fit", "f…
$ draw_id     <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,…
$ p10         <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
$ p25         <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1…
$ p50         <dbl> 3.0, 3.0, 2.5, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0…
$ p75         <dbl> 6, 5, 5, 6, 6, 6, 5, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 6, 6, 6…
$ p90         <dbl> 10, 9, 10, 10, 10, 11, 11, 10, 10, 10, 10, 10, 10, 10, 11,…
$ p99         <dbl> 31.03, 26.10, 26.53, 28.59, 25.69, 29.00, 25.70, 24.60, 23…
$ total_count <int> 2965, 2838, 2863, 2973, 2937, 2992, 2809, 2913, 2916, 2912…
$ mean_count  <dbl> 4.958194, 4.441315, 4.418210, 4.630841, 4.647152, 5.020134…

We now combine all this data to create a number of different comparison plots for the various summary statistics.

Code

#! echo: TRUE

create_multiple_model_assessment_plot(
  obs_summstats_tbl, model_assess_tbl,
  "total_count", "Total Transactions"
  )

Code

create_multiple_model_assessment_plot(
  obs_summstats_tbl, model_assess_tbl,
  "mean_count", "Average Transactions per Customer"
  )

Code

create_multiple_model_assessment_plot(
  obs_summstats_tbl, model_assess_tbl,
  "p99", "99th Percentile Count"
  )

6.1 Write Assessment Data to Disk

We now want to save the assessment data to disk.

Code

model_assess_tbl |> write_rds("data/assess_data_pnbd_onlineretail_fixed_tbl.rds")

R Environment

Code

options(width = 120L)
sessioninfo::session_info()

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       Ubuntu 22.04.3 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Dublin
 date     2023-11-20
 pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package        * version    date (UTC) lib source
 abind            1.4-5      2016-07-21 [1] RSPM (R 4.3.0)
 arrayhelpers     1.1-0      2020-02-04 [1] RSPM (R 4.3.0)
 backports        1.4.1      2021-12-13 [1] RSPM (R 4.3.0)
 base64enc        0.1-3      2015-07-28 [1] RSPM (R 4.3.0)
 bayesplot      * 1.10.0     2022-11-16 [1] RSPM (R 4.3.0)
 bit              4.0.5      2022-11-15 [1] RSPM (R 4.3.0)
 bit64            4.0.5      2020-08-30 [1] RSPM (R 4.3.0)
 bridgesampling   1.1-2      2021-04-16 [1] RSPM (R 4.3.0)
 brms           * 2.20.4     2023-09-25 [1] RSPM (R 4.3.0)
 Brobdingnag      1.2-9      2022-10-19 [1] RSPM (R 4.3.0)
 cachem           1.0.8      2023-05-01 [1] RSPM (R 4.3.0)
 callr            3.7.3      2022-11-02 [1] RSPM (R 4.3.0)
 checkmate        2.3.0      2023-10-25 [1] RSPM (R 4.3.0)
 cli              3.6.1      2023-03-23 [1] RSPM (R 4.3.0)
 cmdstanr       * 0.6.0.9000 2023-11-07 [1] Github (stan-dev/cmdstanr@a13c798)
 coda             0.19-4     2020-09-30 [1] RSPM (R 4.3.0)
 codetools        0.2-19     2023-02-01 [2] CRAN (R 4.3.1)
 colorspace       2.1-0      2023-01-23 [1] RSPM (R 4.3.0)
 colourpicker     1.3.0      2023-08-21 [1] RSPM (R 4.3.0)
 conflicted     * 1.2.0      2023-02-01 [1] RSPM (R 4.3.0)
 cowplot        * 1.1.1      2020-12-30 [1] RSPM (R 4.3.0)
 crayon           1.5.2      2022-09-29 [1] RSPM (R 4.3.0)
 crosstalk        1.2.0      2021-11-04 [1] RSPM (R 4.3.0)
 curl             5.1.0      2023-10-02 [1] RSPM (R 4.3.0)
 digest           0.6.33     2023-07-07 [1] RSPM (R 4.3.0)
 directlabels   * 2023.8.25  2023-09-01 [1] RSPM (R 4.3.0)
 distributional   0.3.2      2023-03-22 [1] RSPM (R 4.3.0)
 dplyr          * 1.1.3      2023-09-03 [1] RSPM (R 4.3.0)
 DT               0.30       2023-10-05 [1] RSPM (R 4.3.0)
 dygraphs         1.1.1.6    2018-07-11 [1] RSPM (R 4.3.0)
 ellipsis         0.3.2      2021-04-29 [1] RSPM (R 4.3.0)
 evaluate         0.22       2023-09-29 [1] RSPM (R 4.3.0)
 fansi            1.0.5      2023-10-08 [1] RSPM (R 4.3.0)
 farver           2.1.1      2022-07-06 [1] RSPM (R 4.3.0)
 fastmap          1.1.1      2023-02-24 [1] RSPM (R 4.3.0)
 forcats        * 1.0.0      2023-01-29 [1] RSPM (R 4.3.0)
 fs             * 1.6.3      2023-07-20 [1] RSPM (R 4.3.0)
 furrr          * 0.3.1      2022-08-15 [1] RSPM (R 4.3.0)
 future         * 1.33.0     2023-07-01 [1] RSPM (R 4.3.0)
 generics         0.1.3      2022-07-05 [1] RSPM (R 4.3.0)
 ggdist           3.3.0      2023-05-13 [1] RSPM (R 4.3.0)
 ggplot2        * 3.4.4      2023-10-12 [1] RSPM (R 4.3.0)
 globals          0.16.2     2022-11-21 [1] RSPM (R 4.3.0)
 glue           * 1.6.2      2022-02-24 [1] RSPM (R 4.3.0)
 gridExtra        2.3        2017-09-09 [1] RSPM (R 4.3.0)
 gtable           0.3.4      2023-08-21 [1] RSPM (R 4.3.0)
 gtools           3.9.4      2022-11-27 [1] RSPM (R 4.3.0)
 hms              1.1.3      2023-03-21 [1] RSPM (R 4.3.0)
 htmltools        0.5.6.1    2023-10-06 [1] RSPM (R 4.3.0)
 htmlwidgets      1.6.2      2023-03-17 [1] RSPM (R 4.3.0)
 httpuv           1.6.12     2023-10-23 [1] RSPM (R 4.3.0)
 igraph           1.5.1      2023-08-10 [1] RSPM (R 4.3.0)
 inline           0.3.19     2021-05-31 [1] RSPM (R 4.3.0)
 jsonlite         1.8.7      2023-06-29 [1] RSPM (R 4.3.0)
 knitr            1.44       2023-09-11 [1] RSPM (R 4.3.0)
 labeling         0.4.3      2023-08-29 [1] RSPM (R 4.3.0)
 later            1.3.1      2023-05-02 [1] RSPM (R 4.3.0)
 lattice          0.21-8     2023-04-05 [2] CRAN (R 4.3.1)
 lifecycle        1.0.3      2022-10-07 [1] RSPM (R 4.3.0)
 listenv          0.9.0      2022-12-16 [1] RSPM (R 4.3.0)
 lobstr         * 1.1.2      2022-06-22 [1] RSPM (R 4.3.0)
 loo              2.6.0      2023-03-31 [1] RSPM (R 4.3.0)
 lubridate      * 1.9.3      2023-09-27 [1] RSPM (R 4.3.0)
 magrittr       * 2.0.3      2022-03-30 [1] RSPM (R 4.3.0)
 markdown         1.11       2023-10-19 [1] RSPM (R 4.3.0)
 Matrix           1.5-4.1    2023-05-18 [2] CRAN (R 4.3.1)
 matrixStats      1.0.0      2023-06-02 [1] RSPM (R 4.3.0)
 memoise          2.0.1      2021-11-26 [1] RSPM (R 4.3.0)
 mime             0.12       2021-09-28 [1] RSPM (R 4.3.0)
 miniUI           0.1.1.1    2018-05-18 [1] RSPM (R 4.3.0)
 munsell          0.5.0      2018-06-12 [1] RSPM (R 4.3.0)
 mvtnorm          1.2-3      2023-08-25 [1] RSPM (R 4.3.0)
 nlme             3.1-162    2023-01-31 [2] CRAN (R 4.3.1)
 parallelly       1.36.0     2023-05-26 [1] RSPM (R 4.3.0)
 pillar           1.9.0      2023-03-22 [1] RSPM (R 4.3.0)
 pkgbuild         1.4.2      2023-06-26 [1] RSPM (R 4.3.0)
 pkgconfig        2.0.3      2019-09-22 [1] RSPM (R 4.3.0)
 plyr             1.8.9      2023-10-02 [1] RSPM (R 4.3.0)
 posterior      * 1.4.1      2023-03-14 [1] RSPM (R 4.3.0)
 prettyunits      1.2.0      2023-09-24 [1] RSPM (R 4.3.0)
 processx         3.8.2      2023-06-30 [1] RSPM (R 4.3.0)
 promises         1.2.1      2023-08-10 [1] RSPM (R 4.3.0)
 ps               1.7.5      2023-04-18 [1] RSPM (R 4.3.0)
 purrr          * 1.0.2      2023-08-10 [1] RSPM (R 4.3.0)
 quadprog         1.5-8      2019-11-20 [1] RSPM (R 4.3.0)
 QuickJSR         1.0.7      2023-10-15 [1] RSPM (R 4.3.0)
 R6               2.5.1      2021-08-19 [1] RSPM (R 4.3.0)
 Rcpp           * 1.0.11     2023-07-06 [1] RSPM (R 4.3.0)
 RcppParallel     5.1.7      2023-02-27 [1] RSPM (R 4.3.0)
 readr          * 2.1.4      2023-02-10 [1] RSPM (R 4.3.0)
 reshape2         1.4.4      2020-04-09 [1] RSPM (R 4.3.0)
 rlang          * 1.1.1      2023-04-28 [1] RSPM (R 4.3.0)
 rmarkdown        2.25       2023-09-18 [1] RSPM (R 4.3.0)
 rstan            2.32.3     2023-10-15 [1] RSPM (R 4.3.0)
 rstantools       2.3.1.1    2023-07-18 [1] RSPM (R 4.3.0)
 rstudioapi       0.15.0     2023-07-07 [1] RSPM (R 4.3.0)
 rsyslog        * 1.0.3      2023-05-08 [1] RSPM (R 4.3.0)
 scales         * 1.2.1      2022-08-20 [1] RSPM (R 4.3.0)
 sessioninfo      1.2.2      2021-12-06 [1] RSPM (R 4.3.0)
 shiny            1.7.5.1    2023-10-14 [1] RSPM (R 4.3.0)
 shinyjs          2.1.0      2021-12-23 [1] RSPM (R 4.3.0)
 shinystan        2.6.0      2022-03-03 [1] RSPM (R 4.3.0)
 shinythemes      1.2.0      2021-01-25 [1] RSPM (R 4.3.0)
 StanHeaders      2.26.28    2023-09-07 [1] RSPM (R 4.3.0)
 stringi          1.7.12     2023-01-11 [1] RSPM (R 4.3.0)
 stringr        * 1.5.0      2022-12-02 [1] RSPM (R 4.3.0)
 svUnit           1.0.6      2021-04-19 [1] RSPM (R 4.3.0)
 tensorA          0.36.2     2020-11-19 [1] RSPM (R 4.3.0)
 threejs          0.3.3      2020-01-21 [1] RSPM (R 4.3.0)
 tibble         * 3.2.1      2023-03-20 [1] RSPM (R 4.3.0)
 tidybayes      * 3.0.6      2023-08-12 [1] RSPM (R 4.3.0)
 tidyr          * 1.3.0      2023-01-24 [1] RSPM (R 4.3.0)
 tidyselect       1.2.0      2022-10-10 [1] RSPM (R 4.3.0)
 tidyverse      * 2.0.0      2023-02-22 [1] RSPM (R 4.3.0)
 timechange       0.2.0      2023-01-11 [1] RSPM (R 4.3.0)
 tzdb             0.4.0      2023-05-12 [1] RSPM (R 4.3.0)
 utf8             1.2.4      2023-10-22 [1] RSPM (R 4.3.0)
 V8               4.4.0      2023-10-09 [1] RSPM (R 4.3.0)
 vctrs            0.6.4      2023-10-12 [1] RSPM (R 4.3.0)
 vroom            1.6.4      2023-10-02 [1] RSPM (R 4.3.0)
 withr            2.5.1      2023-09-26 [1] RSPM (R 4.3.0)
 xfun             0.40       2023-08-09 [1] RSPM (R 4.3.0)
 xtable           1.8-4      2019-04-21 [1] RSPM (R 4.3.0)
 xts              0.13.1     2023-04-16 [1] RSPM (R 4.3.0)
 yaml             2.3.7      2023-01-23 [1] RSPM (R 4.3.0)
 zoo              1.8-12     2023-04-13 [1] RSPM (R 4.3.0)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

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Code

options(width = 80L)